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## D

d - Variable in class org.metaqtl.MetaChrom
  The absolute positions of markers in Morgan.
D - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
D_coeff - Static variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
dataLayers - Variable in class org.metaqtl.graph.MetaGraph
dC - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
dD - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
dE - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
DEFAULT_HEIGHT - Static variable in class org.metaqtl.graph.MetaGraphPar
  The default height.
DEFAULT_WIDTH - Static variable in class org.metaqtl.graph.MetaGraphPar
  The default width.
DEFINITION - Static variable in interface org.thalia.bio.IOntologyTermProperties
  The definition property of a term in a ontology
dF - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
dfridr(NumericalUtilities.Function, double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Returns the derivative of a function func at a point x by Ridders' method of polynomial extrapolation.
dG - Variable in class org.metaqtl.util.OffspringManager.HaldaneWaddingtonProportion
DH - Static variable in interface org.thalia.bio.IBioCrossTypes
disableLogger() - Method in class org.metaqtl.algo.MetaAlgorithm
dist - Variable in class org.metaqtl.TreeNode
  The distance between the node and its parent.
distance(double, int, int) - Static method in class org.metaqtl.util.MappingFunction
  Returns the distance from the recombination rate.
distanceUnitCM - Static variable in interface org.thalia.bio.entity.IGeneticMapProperties
distanceUnitKey - Static variable in interface org.thalia.bio.entity.IGeneticMapProperties
dm - Variable in class org.metaqtl.EMResult
  The matrix of convergence rate for the EM-Algorithm (just for means).
DMAX(double, double) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Returns the max between `a` and `b`
DO_SEM - Static variable in class org.metaqtl.algo.EMAlgorithm
  If true the best starting point is used to do Supplemental EM (SEM) in order to compute the DM Matrix..
doEM(double[], double[], int, EMResult) - Static method in class org.metaqtl.algo.EMAlgorithm
  Apply the EM-Algorithm on the given data set where `x` is an array of observed value and `sd` an array of same size than `x` which stores the standard deviations of the observed values.
DOF - Static variable in interface org.metaqtl.IBioLGroupProperties
  The key for the number of degrees of freedom.
dof - Variable in class org.metaqtl.MetaChrom
  The number of degrees of freedom.
dof - Variable in class org.metaqtl.MultiFitResult
  The number of degrees of freedom.
dominance - Variable in class org.metaqtl.Qtl.QTLStats
  The dominance effect of the QTL.
doProjection(ChromCluster[]) - Method in class org.metaqtl.algo.QtlProjAlgorithm
doQtlClustering(MetaQtlData) - Method in class org.metaqtl.algo.QtlClustAlgorithm
  For a given data set `data` performs the clustering on each trait group and returns the results as an array of `MetaQtlResult` objects.
doTraitGroupClustering() - Method in class org.metaqtl.MetaQtlData
  According to the values of the QTLTrait.group attribute of the trait attribute of the qtls this methos clusterize the qtls in trait groups.
doTraitOntologyClustering(IBioOntology) - Method in class org.metaqtl.MetaQtlData
  According to the given trait ontology this methods clusterize the QTL in group in such a way that each group represents a trait term in the ontology.
draw(Graphics2D) - Method in class org.metaqtl.graph.ChromLayer
draw(Graphics2D) - Method in class org.metaqtl.graph.ChromShape
draw(Graphics2D) - Method in class org.metaqtl.graph.GraphShape
  Draws the shape.
draw(Graphics2D) - Method in class org.metaqtl.graph.Layer
  Draws the layer on the given `graph` context.
draw(Graphics2D, double, double) - Method in class org.metaqtl.graph.MetaGraph
draw(Graphics2D) - Method in class org.metaqtl.graph.QtlLayer
draw(Graphics2D) - Method in class org.metaqtl.graph.QtlPartitionLayer
draw(Graphics2D) - Method in class org.metaqtl.graph.QtlShape
draw(Graphics2D) - Method in class org.metaqtl.graph.QtlTreeLayer
DSWAP(double[], int, int) - Static method in class org.metaqtl.numrec.NumericalUtilities
  Swaps elements i and j in a.
DUBIOUS_ORDER - Static variable in interface org.metaqtl.IBioLocusProperties
  The key for the marker dubious status.
DubiousLocusFactory - Class in org.metaqtl.factory
  A factory to read a list of dubious markers from a file.
DubiousLocusFactory() - Constructor for class org.metaqtl.factory.DubiousLocusFactory

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